Methods to identify patients at risk of developing adverse events during treatment with antidepressant medication

ABSTRACT

The invention provides a method of screening patients to identify those patients more likely to exhibit an increased risk of treatment-emergent suicidal ideation comprising: (a) obtaining a sample of genetic material from the patients, and (b) assaying the sample for the presence of a genotype in the patients which is associated with an increased risk of treatment-emergent suicidal ideation, wherein the genotype is characterized by a polymorphism in a gene selected from the group consisting of glutamine receptor, ionotropic, kainate 2 (GRIK2); glutamate receptor ionotropic AMPA 3 (GRIA3); and combinations thereof.

CROSS-REFERENCE TO RELATED APPLICATIONS

This patent application claims the benefit of U.S. Provisional PatentApplication No. 60/854,978, filed Oct. 27, 2006, and is incorporated byreference herein.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY

Incorporated by reference in its entirety herein is a computer-readablenucleotide/amino acid sequence listing submitted concurrently herewithand identified as follows: One 8,236 Byte ASCII (Text) file named“702157.ST25.TXT,” created on Oct. 25, 2007.

BACKGROUND OF THE INVENTION

Depression is a disease that affects a large proportion of thepopulation and is a result of multiple factors. According to the WorldHealth Organization (WHO), depression ranks among the ten leading causesof disability and will become the second-largest cause of the globalhealth burden by 2020. An estimated 121 million people worldwide sufferfrom a depressive disorder for which they require treatment. It isestimated that 5.8% of all men and 9.5% of all women will suffer from adepressive disorder in any given year and that 17% of all men and womenwill suffer from a depressive disorder at some point in their lives.

Several types of antidepressant medications are used to treat depressivedisorders, such as selective serotonin reuptake inhibitors (SSRIs),tricyclics, and monoamine oxidase inhibitors (MAOIs). The SSRIs andother medications that affect neurotransmitters, such as dopamine andnorepinephrine, generally have fewer side effects than tricyclics.However, studies report a potential link between antidepressant use andthe emergence of suicidal tendencies. According to some studies suicidalideation (SI) is an uncommon but potentially dangerous phenomenon thatcan emerge during antidepressant treatment. Although there is no clearunderstanding of the basis for the observed linkage, the Food and DrugAdministration (FDA) issued a black box warning regarding the potentialrisk of worsening depression and/or emergence of suicidality (i.e.,development of suicidal thoughts or behavior) in both adult andpediatric patients taking several antidepressants.

In view of the FDA's warning, there has been increasing hesitation byphysicians to prescribe antidepressants, particularly to children andadolescents. The need exists for a method to identify individuals atrisk for developing these dangerous side effects. The invention providessuch a method that could provide information about a patient'ssusceptibility for treatment-emergent suicidal ideation (TESI). Theseand other objects and advantages of the invention, as well as additionalinventive features, will be apparent from the description of theinvention provided herein.

BRIEF SUMMARY OF THE INVENTION

The invention provides a method of screening patients to identify thosepatients more likely to exhibit an increased risk of treatment-emergentsuicidal ideation comprising (a) obtaining a sample of genetic materialfrom the patients, and (b) assaying the sample for the presence of agenotype in the patients which is associated with an increased risk oftreatment-emergent suicidal ideation, wherein the genotype ischaracterized by a polymorphism in a gene selected from the groupconsisting of glutamine receptor, ionotropic, kainate 2 (GRIK2);glutamate receptor ionotropic AMPA 3 (GRIA3); and combinations thereof.

DETAILED DESCRIPTION OF THE INVENTION

The biological basis for TESI following treatment with antidepressants,such as SSRIs, previously was unknown. The inventors have determinedthat specific genetic markers can shed light on the causes of TESI andhelp to identify individuals that are at high-risk for TESI and that canbenefit from closer monitoring, alternative treatments, and/or specialtycare.

The inventors utilized the Sequenced Treatment Alternatives to RelieveDepression (STAR*D) trial, which is a large prospective treatment trialfor major depression to test whether specific genetic markers couldpredict TESI in patients treated with the selective serotonin reuptakeinhibitor (SSRI) citalopram.

The inventors identified genetic markers that identify patients at highrisk of developing suicidal thoughts during treatment with the SSRIcitalopram. The markers reside in the genes glutamine receptor,ionotropic, kainate 2 (GRIK2) and glutamate receptor ionotropic AMPA 3(GRIA3).

GRIK2 and GRIA3 encode receptors for the excitatory neurotransmitterglutamate. Glutamate receptors are the predominant excitatoryneurotransmitter receptors in the mammalian brain and are activated in avariety of normal neurophysiologic processes. These receptors areheteromeric protein complexes with multiple subunits, each possessingtransmembrane regions, and all arranged to form a ligand-gated ionchannel. The classification of glutamate receptors is based on theiractivation by different pharmacologic agonists.

GRIK2 encodes a subunit of a kainate glutamate receptor. GRIK2 also isknown as EAA4, GLR6, GLUR6, GLuR-6, and G1uR-6. GRIK2 is located onchromosome 6g16.3-q21. GRIK2 is identified by GenBank Accession NumbersBC037954 and AAH37954, as well as IMAGE clone 5728492.

GRIA3 belongs to a family of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptors. Alternative splicing results in severaldifferent isoforms which may vary in their signal transductionproperties. GRIA3 also is known as GLUR-K3, GLUR3, GLURC, G1uR-3,G1uR-K3, and gluR-C. GRIA3 is located on chromosome Xq25-q26. GRIA3 isidentified by GenBank Accession Numbers BC032004 and AAH32004, as wellas IMAGE clone 4753474.

The invention is directed to a method of screening patients to identifythose patients more likely to exhibit an increased risk oftreatment-emergent suicidal ideation comprising (a) obtaining a sampleof genetic material from the patients, and (b) assaying the sample forthe presence of a genotype in the patients that is associated with anincreased risk of TESI, wherein the genotype is characterized by apolymorphism in a gene selected from the group consisting of GRIK2,GRIA3, and combinations thereof.

TESI refers to the appearance of suicidal thoughts and/or behaviorfollowing treatment, such as treatment with SSRIs. For example, suicidalthoughts and behavior include, but are not limited to, the following:feeling that life is empty and/or wondering if life is worth living;thinking of suicide or death several times a week for several minutes;thinking of suicide or death several times a day in some detail; makingspecific plans for suicide; and attempting or succeeding in taking one'slife.

A patient refers to an individual awaiting or under medical care andtreatment, such as treatment for depression. While the inventive methodsare designed for human patients (e.g., male and female human patients),such methods are applicable to any suitable individual, which includes,but is not limited to, a mammal, such as a mouse, rat, rabbit, hamster,guinea pig, cat, dog, goat, cow, horse, pig, and simian.

The sample of genetic material can be obtained from the patient by anysuitable manner. The sample can be isolated from a source includingsaliva, buccal cells, hair roots, blood, cord blood, amniotic fluid,interstitial fluid, peritoneal fluid, chorionic villus, semen, or othersuitable cell or tissue sample. Methods for isolating genomic DNA fromvarious sources is well-known in the art.

A polymorphism refers to one of multiple alleles of a gene. Preferably,the polymorphism is a single nucleotide polymorphism (SNP).

The polymorphism that is associated with an increased risk of TESI canbe detected by any suitable manner known in the art. For example, thepolymorphism can be detected by techniques, such as allele specifichybridization, allele specific oligonucleotide ligation, primerextension, minisequencing, mass spectroscopy, heteroduplex analysis,single strand conformational polymorphism (SSCP), denaturing gradientgel electrophoresis (DGGE), oligonucleotide microarray analysis,temperature gradient gel electrophoresis (TGGE), and combinationsthereof.

The polymorphism that is associated with an increased risk of TESI inthe GRIK2 gene typically is within intron 1 of GRIK2 (GenBank AccessionNumber NM_(—)021956). In such a situation, intron 1 of GRIK2 typicallycomprises SEQ ID NO: 1, which contains a cytosine at position 201,rather than adenine (which is present in the GRIK2 intron 1 that is notassociated with an increased risk of TESI). This adenine/cytosine SNP isassociated with marker rs2518224 at chromosome 6:102013370.

The polymorphism that is associated with an increased risk of TESI inthe GRIA3 gene typically is within intron 3 of GRIA3 (GenBank AccessionNumber NM_(—)000828). In such a situation, intron 3 of GRIA3 typicallycomprises SEQ ID NO: 2, SEQ ID NO: 3, or SEQ ID NO: 13. SEQ ID NO: 2contains a thymine at position 201, rather than adenine (which ispresent in the GRIA3 intron 3 that is not associated with an increasedrisk of TESI). This adenine/thymine SNP is associated with markerrs6608067 at chromosome X:122151011. SEQ ID NO: 3 contains a guanine atposition 201, rather than adenine (which is present in the GRIA3 genethat is not associated with an increased risk of TEST). Thisadenine/guanine SNP is associated with marker rs4825476 at chromosomeX:122167014. SEQ ID NO: 13 contains a thymine at position 201, ratherthan cytosine (which is present in the GRIA3 intron 3 that is notassociated with an increased risk of TESI). This cytosine/thymine SNP isassociated with marker rs5911588 at chromosome X:122286074.

The invention also comprises assaying for the presence of a genotypethat is associated with an increased risk of TESI, wherein the genotypeis characterized by a polymorphism in a gene selected from the groupconsisting of: glutamate receptor, ionotropic, N-methyl D-aspartate(GRIN) 2A; neurotrophic tyrosine receptor kinase (NTRK) 2;5-hydroxytryptamine (serotonin) receptor (HTR) 3B; GRIA1; papilin(PAPLN); interleukin 28 receptor alpha (IL28RA); and combinationsthereof. Certain polymorphisms in these genes correlate with anincreased risk of developing suicidal thoughts during treatment with theSSRI citalopram.

The polymorphism that is associated with an increased risk of TESI inGRIN2A typically is within intron 3 of GRIN2A (GenBank Accession NumberNM000833). In such a situation, intron 3 of GRIN2A typically comprisesSEQ ID NO: 4, which contains a cytosine at position 201, rather thanadenine (which is present in the GRIN2A gene that is not associated withan increased risk of TESI). This thymine/guanine SNP (opposite strand)is associated with marker rs3104703 at chromosome 16:9972637.

The polymorphism that is associated with an increased risk of TEST inNTRK2 typically is within intron 14 of NTRK2 (GenBank Accession NumberNM_(—)001018064). In such a situation, intron 14 of NTRK2 typicallycomprises SEQ ID NO: 5, which contains a guanine at position 201, ratherthan adenine (which is present in the NTRK2 gene that is not associatedwith an increased risk of TESI). This cytosine/thymine SNP (oppositestrand) is associated with marker rs1573219 at chromosome 9:84617176.

The polymorphism that is associated with an increased risk of TESI inHTR3B typically is within intron 6 of HTR3B (GenBank Accession NumberNM_(—)006028). In such a situation, intron 6 (boundary) of HTR3Btypically comprises SEQ ID NO: 6, which contains a guanine at position201, rather than adenine (which is present in the HTR3B gene that is notassociated with an increased risk of TESI). This adenine/guanine SNP(opposite strand) is associated with marker rs2276307 at chromosome11:113309097.

The polymorphism that is associated with an increased risk of TESI inGRIA1 typically is within intron 5 of GRIA1 (GenBank Accession NumberNM_(—)000827). In such a situation, intron 5 of GRIA1 typicallycomprises SEQ ID NO: 7, which contains a cytosine at position 201,rather than adenine (which is present in the GRIA1 gene that is notassociated with an increased risk of TESI). This adenine/cytosine SNP isassociated with marker rs4958672 at chromosome 5:153028245.

The polymorphism that is associated with an increased risk of TESI inPAPLN typically is within intron 13 of PAPLN (GenBank Accession NumberNM_(—)173462). In such a situation, intron 13 (boundary) of PAPLNtypically comprises SEQ ID NO: 8, which contains a guanine at position201, rather than adenine (which is present in the PAPLN gene that is notassociated with an increased risk of TESI). This adenine/guanine SNP isassociated with marker rs2293796 at chromosome 14:72790915. Similarly,in such a situation, intron 13 (boundary) of PAPLN can comprise SEQ IDNO: 9, which contains a thymine at position 201, rather than a cytosine(which is present in the PAPLN gene that is not associated with anincreased risk of TESI). This cytosine/thymine SNP is associated withmarker rs11628713 at chromosome 14:72791528.

The polymorphism that is associated with an increased risk of TESI inIL28RA typically is within exon 7 or intron 4 of IL28RA (GenBankAccession Number NM_(—)170743). In such a situation, exon 7 of IL28RAtypically comprises SEQ ID NO: 10, which contains a guanine at position201, rather than adenine (which is present in the IL28RA gene that isnot associated with an increased risk of TESI). This adenine/guanine SNPis associated with marker rs10903034 at chromosome 1:24226211.Similarly, exon 7 of IL28RA can comprise SEQ ID NO: 11, which contains athymine at position 201, rather than cytosine (which is present in theIL28RA gene that is not associated with an increased risk of TESI). Thiscytosine/thymine SNP is associated with marker rs11249006 at chromosome1:24227780. Similarly, in such a situation, intron 4 of IL28RA typicallycomprises SEQ ID NO: 12, which contains thymine at position 201, ratherthan cytosine (which is present in the IL28RA gene that is notassociated with an increased risk of TESI). This cytosine/thymine SNP isassociated with marker rs1416834 at chromosome 1:24231966.

Sensitivity is the probability that a symptom is present (or thescreening test is positive) when a patient has a disorder. Thesensitivity of the polymorphism associated with TESI in the inventivemethod can be any suitable sensitivity. Preferably, the sensitivity isabout 0.5 or higher (e.g., about 0.55, about 0.6, about 0.65, about 0.7,about 0.75, about 0.8, about 0.85, about 0.9, about 0.95, and rangesthereof).

Specificity is the probability that a symptom is not present (or thescreening test is negative) when a patient does not have a disorder. Thespecificity of the polymorphism associated with TESI in the inventivemethod can be any suitable specificity. Preferably, the specificity isabout 0.5 or higher (e.g., about 0.55, about 0.6, about 0.65, about 0.7,about 0.75, about 0.8, about 0.85, about 0.9, about 0.95, and rangesthereof).

Positive predictive value is the probability that a patient has adisorder given a positive test result. The positive predictive value ofthe polymorphism associated with TESI in the inventive method can be anysuitable value. Preferably, the positive predictive value is about 0.05or higher (e.g., about 0.1, about 0.2, about 0.25, about 0.3, about 0.4,about 0.5, about 0.55, about 0.6, about 0.65, about 0.7, about 0.75,about 0.8, about 0.85, about 0.9, about 0.95, and ranges thereof).

Negative predictive value is the probability that a patient has thedisorder given a negative test result. The negative predictive value ofthe polymorphism associated with TESI in the inventive method can be anysuitable value. Preferably, the negative predictive value is about 0.5or higher (e.g., about 0.55, about 0.6, about 0.65, about 0.7, about0.75, about 0.8, about 0.85, about 0.9, about 0.95, and ranges thereof).

The invention also contains a kit comprising reagents suitable forapplying the methods of the invention. The kit provides the necessarymaterials for identifying the polymorphism packaged into a suitablecontainer. At a minimum, the kit contains a reagent that identifies apolymorphism in the selected gene that is associated with a selectedtrait, such as TESI. Preferably, the reagent is a set of primers or aPCR set (a set of primers, DNA polymerase, and 4 nucleosidetriphosphates) that hybridizes with the gene or a fragment thereof. Thekit also can include other reagents for detecting or measuring thedetectable entity and/or a control. Other reagents used forhybridization, prehybridization, DNA extraction, visualization, and thelike also can be included.

The following example further illustrates the invention but, of course,should not be construed as in any way limiting its scope.

EXAMPLE

This example demonstrates that genetic markers can be used to identifyindividuals with a major depressive disorder who developtreatment-emergent suicidal ideation (TESI) when exposed to aselective-serotonin reuptake inhibitor (SSRI), such as citalopram.

Experimental Design

DNA was collected from a clinically-representative cohort of 1938outpatients with major depressive disorder enrolled in the SequencedTreatment Alternatives to Relieve Depression (STAR*D) trial. Outpatients18-75 years of age with a baseline 17-item Hamilton Depression RatingScale (see Hamilton et al., J Neurol. Neurosurg. Psychiatry, 23:56-62(1960); and Hamilton, Br. J. Soc. Clin. Psychol., 6 (4):278-296 (1967))(HRSD17) score of ≧14 who met the Diagnostic and Statistical Manual ofMental Disorders (DSM)-IV criteria for non-psychotic major depressivedisorder (MDD) were eligible for the trial.

All participants received initial therapy with citalopram, typicallystarting at 20 mg/day, with dose increases following recommendedprocedures (see Trivedi et al., Am. J. Psychiatry, 163 (1):28-40(2006)). The patients were treated with citalopram under a standardprotocol for up to 14 weeks. DNA was extracted from whole blood andgenotyped on an Illumina Bead Array platform (see Gunderson et al.,Genome Res., 14 (5):870-877 (2004)) for 768 single nucleotidepolymorphisms (SNPs) in 68 candidate genes. Genes were selected tosample five broad signaling pathways of potential importance inantidepressant effects: serotonin (20 genes), glutamate (16 genes),dopamine (3 genes), norepinephrine (4 genes), and neurotrophins (4genes), as well as selected genes in other pathways (21 genes). Allprobands with TESI and a subset of probands without TESI were alsoscreened with the Illumina 109K Exon-Centric chip, which measures thegenotype of a DNA sample at each of 109,000 SNPs in and near most knownhuman genes.

The 16-item Quick Inventory of Depressive Symptomatology—Self-report(QIDS-SR₁₆) was used as a measure of symptom severity (see Rush et al.,Int. J. Methods Psychiatr. Res., 9:45-59 (2000): Rush et al., Biol.Psychiatry, 54 (5): 573-583 (2003); Trivedi et al., Psychol. Med., 34(1):73-82 (2004); Rush et al., Neuropsychompharmacology, 30 (2):405-416(2005); and Rush et al., Biol. Psychiatry, 59 (6):493-501 (2006)) andwas obtained at baseline and at each bi-weekly clinic visit. TEST wasdefined by responses to item 12 of the QIDS-SR₁₆ (“Thoughts of death orsuicide”). Possible responses include: “I do not think of suicide ordeath” (=0), “I feel that life is empty or wonder if it's worth living”(=1), “I think of suicide or death several times a week for severalminutes” (=2), and “I think of suicide or death several times a day insome detail, or I have made specific plans for suicide, or have actuallytried to take my life (=3). Participants who scored “0” on this itembefore citalopram treatment, but who scored 1, 2, or 3 on the same itemat least once while receiving citalopram were defined as TESI cases(n=120). The comparison group (n=1742) consisted of all participants whodenied suicidal ideation emerging during treatment. This includedparticipants who denied suicidal ideation at the initial and subsequentvisits (n=765), as well as those who admitted to suicidal ideation atthe initial visit before commencing treatment, whatever their subsequentreport (n=977). Participants missing suicidal ideation data (n=53) wereexcluded.

Statistical Analysis

Allele and genotype frequencies were compared between the 120participants who developed TESI and those who did not develop TESI.Allele-wise tests are most powerful for alleles that confer risk in aco-dominant or dominant fashion, while genotype-wise tests are morepowerful when a recessive model applies. Allele-wise comparisons wereperformed with Cocaphase in the UNPHASED package (see Dudbridge et al.,Am. J. Hum. Genet., 75 (3):424-435 (2004)), which estimates alikelihood-based test of association under the null hypothesis of allodds ratios (ORs) being equal to one. Genotype-wise comparisons werecarried out using a Pearson Chi-square test on a 2×3 contingency table.Experiment-wise p-values were estimated by permuting case-control labels10,000 times. The number of p-values less than or equal to the lowestp-value observed in the actual data were tallied. Permutation tests wererun separately for autosomal and X-linked markers. Hardy-Weinbergequilibrium for the chosen markers was calculated using PEDSTATS (seeWegginton et al., Bioinformatics, 21(16):3445-3447 (2005)).

SNPs that passed the initial tests with an experiment-wise p<0.05 werestudied further. Tests of association included a logistic regressionmodel calculated with SAS 9.1.3 Enterprise Guide 3.0 (SAS Institute,Cary, N.C.), with a nominal dependent variable for TESI. X-linkedmarkers were separately analyzed in males and females. Single markertests were carried out under co-dominant, dominant, and recessivemodels. Models were compared by the Likelihood Ratio Test (LRT). Thebest-fitting model was used for the multi-marker analyses. The referencemodel was based on the SNPs with the largest identified ORs in thesingle marker models. The remaining covariates were added in a step-wisefashion in descending order of OR. The 2 log-likelihood (−2Log L) wasused to assess the improvement of fit as each variable was removed fromthe model. The Hosmer-Lemeshow test was used to test for final modelfit.

Cases and controls were characterized clinically using bivariatemethods. Differences between groups were tested by Chi-square statisticsfor nominal and ordinal variables and by t-statistics for continuousvariables.

Results

Two markers were significantly associated with TESI. A marker in thegene GRIK2 on chromosome 6 (marker 157), which encodes the type 6glutamate receptor, was associated with TESI in the genotype-wise test(nominal p=2.43×10⁻⁵; permutation p<0.003). This marker was notsignificantly associated in the allele-wise test, but three othermarkers in this gene produced nominally-significant evidence of allelicassociation.

A second marker, in the gene GRIA3 on chromosome X (marker 239), whichencodes an AMPA receptor, was associated with TESI in the allele-wisetest (nominal p=7.84×10⁻⁵; permutation p<0.01). The genotype-wise testof this marker also produced nominally-significant evidence ofassociation in females (p=0.0062), as did allele-wise tests of fournearby markers in this gene.

Having established experiment-wise significant associations between thetwo markers and TESI, the impact of non-genetic variables, such as race,on the observed genetic association was investigated. Table 1 includesdemographic and clinical data for the 120 participants and the 1742controls.

TABLE 1 Demographic and Clinical Data. Cases (n = 120) Controls (n =1742) N (%)   N (%)  df χ² p Variable Gender (female) 71 (59.2) 1072(61.5)  1 0.2664  NS^(a) Race 2 1.0563 NS White 91 (75.8) 1382 (79.3) Black 20 (16.7) 262 (15.0) Other 9 (7.5) 98 (5.6) Hispanic (No) 102(85.0)  1501 (86.2)  1 0.1273 NS Employment 2 1.9630 NS Employed 64(53.3) 981 (56.3) Retired 6 (5.0) 129 (7.4)  Unemployed 50 (41.7) 632(36.3) Marital status 3 0.6588 NS Married 52 (43.3) 745 (42.8) Divorced33 (27.5) 435 (25.0) Never Married 31 (25.8) 492 (28.2) Widowed 4 (3.3)70 (4.0) Clinical Characteristics - Categorical Remission by QIDS-C^(b)(No) 90 (75.6) 994 (57.2) 1 15.529 <0.0001  Psychomotor Agitation (No)104 (86.7)  1508 (86.6)  1 0.0010 NS (QIDS-SR₁₆ item 16) InitialInsomnia (No) 104 (86.7)  1530 (87.8)  1 0.1414 NS (QIDS-SR₁₆ item 1)Drug Abuse (No)^(c) 109 (93.2)  1618 (94.0)  1 0.1404 NS Alcohol Abuse(No)^(c) 105 (89.0)  1543 (89.5)  1 0.0254 NS History of SuicideAttempts (No) 101 (84.2)  1481 (85.1)  1 0.0713 NS MedicationTolerability^(d) 3 3.1386 NS Intolerant 12 (10.1) 198 (11.4) ProbablyIntolerant 2 (1.7) 34 (1.9) Probably Tolerant 26 (21.9) 273 (15.7)Tolerant 79 (66.4) 1232 (70.9)  Level 1 exit 2 14.834 0.0006 Follow Up35 (29.2) 805 (46.2) Next Level 75 (62.5) 782 (44.9) Study Exit 10(8.3)  155 (8.9)  Clinical characteristics - Cases (n = 120) Controls (n= 1742) Continuous Mean (SD)    Mean (SD)   t p Maximum Citalopram Dose(mg/d) 51.75 (13.7)   46.22 (15.3)  3.86 0.0001 Age at Onset of FirstMDE (yrs.) 24.31 (15.8)   25.89 (15.0)  −1.12 NS Age at enrollment(yrs.) 42.26 (13.3)   42.54 (13.4)  −0.22 NS ^(a)Not significant^(b)Defined as score of 5 or less on the last recorded visit. ^(c)Basedon self-report responses to the Psychiatric Diagnostic ScreeningQuestionnaire set at 90% specificity (see Rush et al., J. Affect.Disord., 87(1): 43-55 (2005)). ^(d)As defined by the algorithm detailedin McMahon et al. (Am. J. Hum. Genet., 78(5): 804-814 (2006)).

The best-fitting model was achieved with a combination of both markers,maximum citalopram dose, and remission by the 16-Item Quick Inventory ofDepressive Symptomatology (QIDS)—Clinician Rating (QIDS-C). Race was nota significant covariate in this model. Adjusted ORs were very close tothose in the unadjusted models. The Hosmer-Lemeshow test wasnon-significant for both genders, indicating a good model fit.

Tables 2 and 3 demonstrate logistic regression models with stepwiseselection for the two markers, wherein race was forced into each model.

TABLE 2 Logistic Regression Model for Females (n = 70 cases, 1067controls). Step Model variables −2Log L LR χ² df p-value 1 marker 157and race 519.6 6.3 3 0.0982 2 marker 157, remission, race 512.2 13.7 40.0084 3 marker 157, marker 239, 505.2 20.7 5 0.0009 remission, racewherein LR = likelihood ratio, df = degrees of freedom. The c index forthis model is 0.64.

TABLE 3 Logistic Regression Model for Males (n = 49 cases, 670controls). Step Model variables −2Log L LR χ² df p-value 1 marker 157and race 346.5 11.3 3 0.01 2 marker 157, maximum 334.1 23.8 4 <.0001citalopram dose, race 3 marker 157, maximum 327.8 30.1 5 <.0001citalopram dose, marker 239, race 4 marker 157, marker 323.0 34.8 6<.0001 239, maximum citalopram dose, remission, race The c index forthis model is 0.73.

The clinical parameters for markers 157 and 239 are reported in Table 4.The high-risk genotype of marker 157 correlates with a SNP in intron 1of GRIK2 (e.g., SEQ ID NO: 1). The high-risk alleles of marker 239contain a SNP in intron 3 of GRIA3 (e.g., SEQ ID NOs: 2 and 3). Of thesix combinations of high-risk alleles and genotypes tested, the highestOR was observed in patients carrying both the high-risk alleles ofmarker 239 and the high-risk genotype of marker 157 (OR=14.98, 95%Confidence Interval (CI)=3.7, 60.674). Although only 8 patients carriedit, this particular combination of alleles had 99.8% specificity forTESI. The most sensitive test (57%) required the presence of one or morehigh-risk alleles of marker 239 only. The combined impact of bothmarkers on TESI risk appears to be at least additive, but sample sizeprecludes any precise estimates of the mode of interaction.

TABLE 4 Clinical parameters for Markers 157 and 239. Positive Negative95% Predictive Predictive Prevalence Model OR CI Sensitivity SpecificityValue Value Ratio (1) marker 8.23  3.224, 21.057 0.06 0.993 0.35 0.945.71 157, high-risk genotype (2) marker 1.94 1.33, 2.82 0.57 0.59 0.090.95 1.85 239, ≧ one high- risk allele (3) marker 2.19 1.45, 3.32 0.290.84 0.11 0.95 2.06 239, two high- risk alleles Both (1) and 8.55  2.47,29.62 0.03 0.996 0.36 0.94 5.82 (2) Either (1) or 2.38 1.59, 3.57 0.320.84 0.12 0.95 2.22 (3) Both (1) and 14.9  3.70, 60.67 0.033 0.998 0.500.94 7.99 (3)

The identified markers, taken together, predict TESI in this sample withhigh specificity, but only moderate sensitivity. This is not surprisinggiven the relatively small number of genes tested and the likelycontribution of non-genetic factors to TESI risk. Nevertheless, thefindings have several direct clinical implications.

These markers can help identify patients at high risk for TESI. Suchpatients will benefit from closer monitoring, alternative treatments,and/or specialty care. Such testing can allay the concern that has ledregulatory agencies to issue warnings that contribute to a decrease inantidepressant prescriptions for patients who could benefit from them.Rather than broad warnings that can inappropriately affectantidepressant prescribing practices, identification of these markersindicates that narrower warnings could be appropriate that bettercapture the heterogeneous nature of TESI risk in those patients treatedwith antidepressants. These findings suggest that at least some of thatheterogeneity has a genetic basis.

Several other markers were identified that correlate with an increasedrisk of TESI. These markers were identified in the following genes:GRIN2A, NTRK2, HTR3B, GRIA1, and PAPLN. SNPs in intron 3 of GRIN2A(e.g., SEQ ID NO: 4), intron 14 of NTRK2 (e.g., SEQ ID NO: 5), intron 16of HTR3B (e.g., SEQ ID NO: 6), intron 5 of GRIA1 (SEQ ID NO: 7), andintron 13 of PAPLN (e.g., SEQ ID NOs: 8 or 9) were associated withincreased risk of TESI in those treated with citalopram.

In particular, markers in PAPLN (marker rs11628713) and IL28RA (markerrs10903034) were significant at the p=0.01 and p=0.06 levels,respectively, in an evaluation of 90 TESI cases and 90 matched controls.

All references, including publications, patent applications, andpatents, cited herein are hereby incorporated by reference to the sameextent as if each reference were individually and specifically indicatedto be incorporated by reference and were set forth in its entiretyherein.

The use of the terms “a” and “an” and “the” and similar referents in thecontext of describing the invention (especially in the context of thefollowing claims) are to be construed to cover both the singular and theplural, unless otherwise indicated herein or clearly contradicted bycontext. The terms “comprising,” “having,” “including,” and “containing”are to be construed as open-ended terms (i.e., meaning “including, butnot limited to,”) unless otherwise noted. Recitation of ranges of valuesherein are merely intended to serve as a shorthand method of referringindividually to each separate value falling within the range, unlessotherwise indicated herein, and each separate value is incorporated intothe specification as if it were individually recited herein. All methodsdescribed herein can be performed in any suitable order unless otherwiseindicated herein or otherwise clearly contradicted by context. The useof any and all examples, or exemplary language (e.g., “such as”)provided herein, is intended merely to better illuminate the inventionand does not pose a limitation on the scope of the invention unlessotherwise claimed. No language in the specification should be construedas indicating any non-claimed element as essential to the practice ofthe invention.

Preferred embodiments of this invention are described herein, includingthe best mode known to the inventors for carrying out the invention.Variations of those preferred embodiments may become apparent to thoseof ordinary skill in the art upon reading the foregoing description. Theinventors expect skilled artisans to employ such variations asappropriate, and the inventors intend for the invention to be practicedotherwise than as specifically described herein. Accordingly, thisinvention includes all modifications and equivalents of the subjectmatter recited in the claims appended hereto as permitted by applicablelaw. Moreover, any combination of the above-described elements in allpossible variations thereof is encompassed by the invention unlessotherwise indicated herein or otherwise clearly contradicted by context.

1. A method of screening patients to identify those patients more likelyto exhibit an increased risk of treatment-emergent suicidal ideationcomprising: (a) obtaining a sample of genetic material from thepatients, and (b) assaying the sample for the presence of a genotype inthe patients which is associated with an increased risk oftreatment-emergent suicidal ideation, wherein the genotype ischaracterized by a polymorphism in a gene selected from the groupconsisting of glutamine receptor, ionotropic, kainate 2 (GRIK2);glutamate receptor ionotropic AMPA 3 (GRIA3); and combinations thereof.2. The method of claim 1, wherein assaying comprises detecting thepolymorphism by allele specific hybridization, allele specificoligonucleotide ligation, primer extension, minisequencing, massspectroscopy, heteroduplex analysis, single strand conformationalpolymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE),oligonucleotide microarray analysis, temperature gradient gelelectrophoresis (TGGE), and combinations thereof.
 3. The method of claim1, wherein the gene is GRIK2.
 4. The method of claim 3, wherein thepolymorphism is within intron 1 of GRIK2.
 5. The method of claim 4,wherein intron 1 of GRIK2 comprises SEQ ID NO:
 1. 6. The method of claim1, wherein the gene is GRIA3.
 7. The method of claim 6, wherein thepolymorphism is within intron 3 of GRIA3.
 8. The method of claim 7,wherein intron 3 of GRIA3 comprises SEQ ID NO: 2, SEQ ID NO: 3, or SEQID NO:
 13. 9. The method of claim 1, further comprising assaying for thepresence of a genotype in the patients which is associated with anincreased risk of treatment-emergent suicidal ideation, wherein thegenotype is characterized by a polymorphism in a gene selected from thegroup consisting of glutamate receptor, ionotropic, N-methyl D-aspartate(GRIN) 2A; neurotrophic tyrosine receptor kinase (NTRK) 2;5-hydroxytryptamine (serotonin) receptor (HTR) 3B, GRIA1; papilin(PAPLN); interleukin 28 receptor alpha (IL28RA); and combinationsthereof.
 10. The method of claim 9, wherein assaying for the presence ofthe genotype comprises detecting the presence of SEQ ID NO: 4, SEQ IDNO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ IDNO: 10, SEQ ID NO: 11, SEQ ID NO 12, or combinations thereof.
 11. Amethod of screening patients to identify those patients more likely toexhibit an increased risk of treatment-emergent suicidal ideationcomprising: (a) obtaining a sample of genetic material from thepatients, and (b) assaying the sample for the presence of a genotype inthe patients which is associated with an increased risk oftreatment-emergent suicidal ideation, wherein the genotype ischaracterized by a polymorphism in a gene selected from the groupconsisting of glutamate receptor, ionotropic, N-methyl D-aspartate(GRIN) 2A; neurotrophic tyrosine receptor kinase (NTRK) 2;5-hydroxytryptamine (serotonin) receptor (HTR) 3B, GRIA1; papilin(PAPLN); interleukin 28 receptor alpha (IL28RA); and combinationsthereof.
 12. The method of claim 11, wherein assaying comprisesdetecting the polymorphism by allele specific hybridization, allelespecific oligonucleotide ligation, primer extension, minisequencing,mass spectroscopy, heteroduplex analysis, single strand conformationalpolymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE),oligonucleotide microarray analysis, temperature gradient gelelectrophoresis (TGGE), and combinations thereof.
 13. The method ofclaim 11, wherein the gene is GRIN2A.
 14. The method of claim 13,wherein the polymorphism is within intron 3 of GRIN2A.
 15. The method ofclaim 11, wherein the gene is NTRK2.
 16. The method of claim 15, whereinthe polymorphism is within intron 14 of NTRK2.
 17. The method of claim11, wherein the gene is HTR3B.
 18. The method of claim 17, wherein thepolymorphism is within intron 6 of HTR3B.
 19. The method of claim 11,wherein the gene is GRIA1.
 20. The method of claim 19, wherein thepolymorphism is within intron 5 of GRIA1.
 21. The method of claim 11,wherein the gene is PAPLN.
 22. The method of claim 21, wherein thepolymorphism is within intron 13 of PAPLN.
 23. The method of claim 11,wherein the gene is IL28RA.
 24. The method of claim 23, wherein thepolymorphism is within exon 7 of IL28RA.
 25. The method of claim 23,wherein the polymorphism is within intron 4 of IL28RA.